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opennotspecifiedMar 2006View details →

List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records in A new species of bat of the Hipposideros bicolor group (Chiroptera: Hipposideridae) from Central Laos, with evidence of convergent evolution with Sundaic taxa

List of tissue specimens of Hipposideros spp. used for cytochrome b sequencing and phylogenetic inference, with geographical data. Voucher refers to the location and/or accession number of the voucher, and tissue collection refers to the collection where the tissue is kept, and accession or collector numbers. Acronyms are as follows: Estación Biológica de DoZana, Sevilla, Spain (EBD), South Australia Museum, Adelaide, Australia (SAM), Senckenberg Museum, Frankfurt am Main, Germany (SMF), Instituto de Ecología, Xalapa, México (IEX), Louisiana State University, Baton Rouge, Louisiana, USA (LSU), Charles M. Francis, Canadian Wildlife Service, Ottawa, Ontario, Canada (CMF), Lao Department of Forestry, Vientiane, Lao PDR, no catalogued (LAO). Next column indicates GenBank accession numbers. More information about the specimens is available in the GenBank records

opencc-zeroDec 2014View details →

Data from: Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing

Many phylogenomic studies based on transcriptomes have been limited to "single-copy" genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup taxa. By decomposing these homolog trees, and taking gene duplications into account, we obtained 17,273 ortholog groups, where each was represented by at least ten ingroup taxa. We reconstructed the species phylogeny using a 1,122-gene data set with a gene occupancy of 92.1%. From the homolog trees, we found that both synonymous and nonsynonymous substitution rates in herbaceous lineages are up to three times as fast as in their woody relatives. This is the first time such a pattern has been shown across thousands of nuclear genes with dense taxon sampling. We also pinpointed regions of the Caryophyllales tree that were characterized by relatively high frequencies of gene duplication, including three previously unrecognized whole-genome duplications. By further combining information from homolog tree topology and synonymous distance between paralog pairs, phylogenetic locations for 13 putative genome duplication events were identified. Genes that experienced the greatest gene family expansion were concentrated among those involved in signal transduction and oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme in the betalain synthesis pathway. Our approach demonstrates a new approach for functional phylogenomic analysis in nonmodel species that is based on homolog groups in addition to inferred ortholog groups.

opencc-zeroDec 2015View details →

Data from: The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera

Background: The eusocial Hymenoptera have radiated across a wide range of thermal environments, exposing them to significant physiological stressors. We reconstructed the evolutionary history of three families of Heat Shock Proteins (Hsp90, Hsp70, Hsp40), the primary molecular chaperones protecting against thermal damage, across 12 Hymenopteran species and four other insect orders. We also predicted and tested for thermal inducibility of eight Hsps from the presence of cis-regulatory heat shock elements (HSEs). We tested whether Hsp induction patterns in ants were associated with different thermal environments. Results: We found evidence for duplications, losses, and cis-regulatory changes in two of the three gene families. One member of the Hsp90 gene family, hsp83, duplicated basally in the Hymenoptera, with shifts in HSE motifs in the novel copy. Both copies were retained in bees, but ants retained only the novel HSE copy. For Hsp70, Hymenoptera lack the primary heat-inducible orthologue from Drosophila melanogaster and instead induce the cognate form, hsc70-4, which also underwent an early duplication. Episodic diversifying selection was detected along the branch predating the duplication of hsc70-4 and continued along one of the paralogue branches after duplication. Four out of eight Hsp genes were heat-inducible and matched the predictions based on presence of conserved HSEs. For the inducible homologues, the more thermally tolerant species, Pogonomyrmex barbatus, had greater Hsp basal expression and induction in response to heat stress than did the less thermally tolerant species, Aphaenogaster picea. Furthermore, there was no trade-off between basal expression and induction. Conclusions: Our results highlight the unique evolutionary history of Hsps in eusocial Hymenoptera, which has been shaped by gains, losses, and changes in cis-regulation. Ants, and most likely other Hymenoptera, utilize lineage-specific heat inducible Hsps, whose expression patterns are associated with adaptive variation in thermal tolerance between two ant species. Collectively, our analyses suggest that Hsp sequence and expression patterns may reflect the forces of selection acting on thermal tolerance in ants and other social Hymenoptera.

opencc-zeroDec 2013View details →

Data from: Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages

Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modelled accurately using the Γ distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or under-parameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10,000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42,337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these 3 sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modelled by a combination of 8 edge-specific rate matrices (4 for V1 and 4 for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the 7 species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species.

opencc-zeroSep 2019View details →

Data from: Exploring evolution and diversity of Chinese Dipterocarpaceae using next-generation sequencing

Tropical forests, a key-category of land ecosystems, are faced with the world's highest levels of habitat conversion and associated biodiversity loss. In tropical Asia, Dipterocarpaceae are one of the economically and ecologically most important tree families, but their genomic diversity and evolution remain understudied, hampered by a lack of available genetic resources. Southern China represents the northern limit for Dipterocarpaceae, and thus changes in habitat ecology, community composition and adaptability to climatic conditions are of particular interest in this group. Phylogenomics is a tool for exploring both biodiversity and evolutionary relationships through space and time using plastome, nuclear and mitochondrial genome. We generated full plastome and Nuclear Ribosomal Cistron (NRC) data for Chinese Dipterocarpaceae species as a first step to improve our understanding of their ecology and evolutionary relationships. We generated the plastome of Dipterocarpus turbinatus, the species with the widest distribution using it as a baseline for comparisons with other taxa. Results showed low level of genomic diversity among analysed range-edge species, and different evolutionary history of the incongruent NRC and plastome data. Genomic resources provided in this study will serve as a starting point for future studies on conservation and sustainable use of these dominant forest taxa, phylogenomics and evolutionary studies.

opencc-by-4.0Nov 2021View details →

Supplementary File to "Both binding strength and evolutionary accessibility affect the population frequency of transcription factor binding sequences in Arabidopsis thaliana" (Genome Biology and Evolution)

This data is supplementary file 1 of the following publication: Schweizer G, Wagner A. "Both binding strength and evolutionary accessibility affect the population frequency of transcription factor binding sequences in Arabidopsis thaliana" (Genome Biology and Evolution)

opencc-by-4.0Jul 2022View details →

Supplementary Data for "Phosphorus variations in volcanic sequences reveal the linkage between regional tectonics and terrestrial biota evolution" in G-Cubed.

Supplementary data tables for Ma et al. (2022) associated with the paper entitled "Phosphorus variations in volcanic sequences reveal the linkage between regional tectonics and terrestrial biota evolution" published in G-Cubed.

opencc-zeroAug 2022View details →

Data from: Phylogenetic inferences using nuclear ribosomal ITS and chloroplast sequences provide insights into the biogeographic origins, diversification timescales and trait evolution of Rubus in the Japanese Archipelago

This study aimed to reveal the evolutionary timescale and processes underlying the diversity of Rubus in the Japanese Archipelago. We conducted molecular phylogenetic analyses of most native species (35 species), along with previously published data from 116 foreign species, based on nuclear ribosomal internal transcribed spacer (ITS) and chloroplast DNA sequences. Most of the northern species of Japan, that is, R. chamaemorus, R. pedatus, R. vernus, R. pseudojaponicus, and R. ikenoensis, were found to belong to anciently diverged lineages; in particular, R. ikenoensis formed a unique lineage distinct from other species. The other species diverged into two evolutionary groups. One included subg. Malachobatus, Chamaebatus, and sects. Pungentes, Idaeanthi, and Parvifolii (subg. Idaeobatus), which was further divided into two clades in the chloroplast phylogenies. Although the phylogenetic structures within this group were unresolved, R. sieboldii has been proven to be recently derived. The second group represented a well-supported clade, comprising sects. Microphylli, Corchorifolii, Peltati, and Rosifolii (subg. Idaeobatus), and suggested early Miocene diversification of this Asian lineage associated with character specialization in vegetative reproduction and leaf shape. This clade was further resolved into lower clades primarily representing the sectional classifications, although the placement of the earliest diverged species, R. sumatranus, R. peltatus, R. corchorifolius, and R. chingii, was incongruent among gene trees. At the lower taxonomic levels, R. illecebrosus, R. grayanus, and the thornless species of sect. Microphylli showed earlier divergence.

opencc-by-4.0Apr 2024View details →

The composite metamorphic sequence in the Jiajika gneiss dome, Songpan-Ganze orogenic belt, eastern Tibet: P–T–D–t evolution and implications for lithium mineralization

This is the dataset for "The composite metamorphic sequence in the Jiajika gneiss dome, Songpan-Ganze orogenic belt, eastern Tibet: P–T–D–t evolution and implications for lithium mineralization". The dataset includes EMPA, whole-rock major elements, and geochronological data.

opencc-by-4.0May 2024View details →

Zircon constraints on the eruptive sequence and magma evolution of rhyolites at South Sister volcano, Oregon

This is the repository for data used for analysis in “Zircon constraints on the eruptive sequence and magma evolution of rhyolites at South Sister volcano, Oregon” submitted to Geochemistry, Geophysics, Geosystems. There are four datafiles. Dechert_TableS1.xlsx includes rock sample unit information and locations. Dechert_TableS2.xlsx includes the 230Th-238U isotope ratios as collected with the Stanford-USGS SHRIMP-RG, the isochron model slope and ages, and the Boehnke model slope and ages (Boehnke et al., 2016). Dechert_TableS3.xlsx includes the trace element and rare earth element concentrations collected with the Stanford-USGS SHRIMP-RG. Dechert_TableS4.xlsx records whole rock data for a split of the zircon rock samples collected at Hamilton Analytical Lab and Washington State University.

opencc-by-4.0Feb 2018View details →

Sequencing data for "Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays"

Illumina and Oxford Nanopore sequencing datasets (in FASTQ format) generated for the manuscript "Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays." Paired-end Illumina MiSeq data are uploaded as two separate files ("r1" and "r2") for each passaged population. BAM files, filtered to exclude reads that did not align to K3L, are provided for passaged populations analyzed in the manuscript.

Fig. 6 in Skeletogenesis and sequence heterochrony in rodent evolution, with particular emphasis on the African striped mouse, Rhabdomys pumilio (Mammalia)

Fig. 6 Camera lucida drawings of the right hand (shown at left) and foot, in dorsal views, of Rhabdomys pumilio. Autopodial elements: as = astragalus, ca = calcaneus, ce = centrale, dc = distal carpal, dt = distal tarsal, f = fibula, mc = metacarpal, mt = metatarsal, nv = navicular, pi = pisiform, r = radius, sc = scaphoid, u = ulna, t = tibia, tr = triquetrum. Scales: 2 mm

Fig. 3 in Skeletogenesis and sequence heterochrony in rodent evolution, with particular emphasis on the African striped mouse, Rhabdomys pumilio (Mammalia)

Fig. 3 Cleared and double-stained rodents prepared at the Paläontologisches Institut, Zürich. Left: Octodon degus. Right: Rhabdomys pumilio. Scale: 2 mm

Fig. 4 in Skeletogenesis and sequence heterochrony in rodent evolution, with particular emphasis on the African striped mouse, Rhabdomys pumilio (Mammalia)

Fig. 4 Ossification of elements of the left hand (respective up- per row) and foot (lower row), in dorsal views, of Rhabdomys pumilio; black = ossified, grey = calcified. Number of specimens examined (N)= 1, except at stages a (N =16), f (6), g (2), n (9), y (4), and z (2)

Fig. 1 in Skeletogenesis and sequence heterochrony in rodent evolution, with particular emphasis on the African striped mouse, Rhabdomys pumilio (Mammalia)

Fig. 1 Phylogenetic relationships among the species includ- ed in this study, reconstructed from Steppan et al. (2004), Bininda-Emonds et al. (2007), and Blanga-Kanfi et al. (2009)

Fig. 2 A in Skeletogenesis and sequence heterochrony in rodent evolution, with particular emphasis on the African striped mouse, Rhabdomys pumilio (Mammalia)

Fig. 2 A sample of ontogenetic series prepared for this study at the Paläontologisches Institut und Museum, Zürich. a Cavia porcellus. b Rhabdomys pumilio. c Octodon degus. Scales: 2 mm

opencc-by-4.0Jul 2024View details →

Associated data for "Optimisation strategies for directed evolution without sequencing"

Associated publication available at https://www.biorxiv.org/content/10.1101/2024.03.18.585521v1. Code for visualisation available at https://github.com/nesou2/direvo_sim (PLOS_figures/PLOS_figures.ipynb).